fastaExtractNseqs.py

#!/usr/bin/env python3

import sys


def help():
    print('''
        Usage:
        ------------
        fastaExtractNseqs.py -fasta <file> -n <int> -j <int>

        Description:
        ------------
        Prints the jth n sequences from the FASTA file. -n 2 -j 2 would 
        output the second two sequences.

        Options:
        ------------
        -fasta <file>   The input fasta file
        -n     <int>    The number of sequences to output
        -j     <int>    The set of sequences to output. e.g:
                        -j 1 means output the first n seqs
                        -j 2 menas output the second n seqs
        ''')
    sys.exit(0)


# output help information if missing command line arguments
args = sys.argv
if (not len(args) == 7 
    or not '-j' in args 
    or not '-n' in args 
    or not '-fasta' in args):
    help()
# read command line argument
in_fl = open(args[args.index('-fasta') + 1])
n = int(args[args.index('-n') + 1])
j = int(args[args.index('-j') + 1])
ct = 0
j_ct = 1
for line in in_fl:
    # increment n at seq headers
    if line.startswith('>'):
        ct += 1
        # increment j if count reaches n
        if ct > n: 
            ct = 1
            j_ct += 1
        if j_ct < j:
            continue
        elif j_ct == j:
            print(line.strip())
        # stop if past the jth set of n
        elif j_ct > j:
            break
    else:
        if j_ct == j:
            print(line.strip())
        else:
            continue